WASHINGTON — In a secret meeting held in late 1963, a top US diplomat was “particularly interested” in Attorney General Robert F. Kennedy’s views about implementing another blockade of communist Cuba, which new intelligence suggested may have shipped arms to guerrillas in Venezuela.Kennedy, who was still mourning the assassination a few weeks earlier of his brother, President John F. Kennedy, was not present for the session of the so-called “Special Group” that he chaired to coordinate covert operations. The sensitive discussion was recounted to him in a confidential memo from a top aide. “What measures are we capable of taking and what measures should we take?” Justice Department official John Nolan asked Robert Kennedy in the Dec. 9, 1963 memo, which remained classified until an appeal for its release filed by the Globe was recently granted.But how exactly — or even whether — Kennedy responded to the query is not revealed.Despite steps by the National Archives and Kennedy’s heirs to make public dozens of boxes of the attorney general’s “confidential” and “classified” files, numerous memos, reports, and other correspondence have been removed pending review by the CIA and military branches, according to researchers and government archivists. They cited the need to protect national security. That has included some files about the Special Group’s deliberations between September and December 1963, a highly sensitive period before and after President Kennedy’s assassination in Dallas on Nov. 22, when concerns were highest that a foreign power or CIA-backed Cuban exiles might have been involved or had knowledge about the assassination.For decades the John F. Kennedy Library and Museum in Dorchester, which is part of the National Archives, and the Kennedy family wrangled with historians and journalists who were anxious to glean new insights from some 60 boxes of unopened RFK files covering his term as the nation’s top law enforcement officer from 1961 to 1964.That time frame covers a critical period of the Cold War in which the younger Kennedy played an influential role as confidant to the president and overseer of covert plots, including attempts to overthrow Cuba’s president, Fidel Castro.The controversy over the files appeared to have been settled in 2012 and 2013, when the boxes were opened so “the public will benefit from exploring these documents,” as the chief archivist of the United States, David Ferriero, put it at the time.But as the yearlong effort by the Globe to win the release of a relatively innocuous two-page memo illustrates, many files are still withheld, which has frustrated researchers and specialists on the government classification system.“This document contains not a single substantive secret — no names of CIA agents; no sources and methods, no cryptonyms of actual covert operations — nothing that would warrant it being withdrawn and withheld from the file to begin with,” said Peter Kornbluh, a senior analyst and head of the Cuba Documentation Project at the National Security Archive at George Washington University, after reviewing the newly released Nolan memo to Kennedy.He added: “The fact that the document was withheld in its entirety is an indication of how flawed and arbitrary the secrecy system remains.”The Kennedy Library, where the former attorney general’s files have resided for more than four decades, was required by a 1973 agreement to get permission from Robert Kennedy’s heirs before making the documents available.That permission was granted in 2012. But many files contained secret government documents and the national security agencies that originally classified the information retained the ultimate authority to release them.The JFK Library has not estimated how many files in Robert Kennedy’s attorney general papers are being withheld, according to director Tom Putnam. But he acknowledged that a “good number” of documents have been withdrawn.Putnam said in an e-mail that the library has “opened as many documents as possible in order to open the material to researchers. . . . Other documents that could not be declassified by our in-house staff have been sent to the various agencies that have equity in the documents.”The CIA, which has purview over many of the withheld files, did not respond to a request for comment.One category contained the agenda and minutes of the so-called Special Group — its formal name was Special Group (CI), for “counter insurgency” — during the last quarter of 1963.The Special Group, headed by Robert Kennedy, had purview over covert operations targeting communist infiltrators around the world. As the Nolan memo recounted, on any given day topics ranged from “terrorist operations in Latin America” to new arms being acquired by Viet Cong guerrillas in Vietnam.Some historians have raised questions about whether withheld documents about the Special Group in late 1963 might contain sensitive new details of anti-Cuba operations and other deliberations taking place around the time of the president’s assassination.Some key documents from that period were withheld even though most of the Special Group’s agendas and meeting minutes between 1962 and 1964 were opened.Kornbluh, co-author of the new book “Back Channel to Cuba: The Hidden History of Negotiations between Washington and Havana,” was critical of the lack of disclosure.“The Special Group was in charge of covert operation and the CIA still wants to hide covert operations that happened over 50 years ago from the American public,” he said.Bryan Bender can be reached at bryan.bender@globe.com. Follow him on Twitter@GlobeBender.